Issue 695: Upgrade script version of fixing container for sample files that have moved #7365
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…s that have moved
cnathe
approved these changes
Jan 28, 2026
| GROUP BY DataFileUrl) c | ||
| WHERE c.count > 1))"""); | ||
| WHERE c.count > 1)) | ||
| AND datafileurl LIKE '%/sampletype/%'"""); |
Contributor
There was a problem hiding this comment.
unrelated to this line, but the logging for this upgrade script seems excessive. I am getting the "Ensuring file data in container /Assay Security Test" INFO log for every container in my server, twice! Seems like we could take that log info statement out?
Contributor
Author
There was a problem hiding this comment.
Yes, you are right. I noticed that too and thought it of questionable utility.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Rationale
While investigating approach for allowing deletion of files associated with samples that have become obsolete (Issue 695), it was discovered that when samples are moved from one container to another, the container field in
exp.datawas not getting updated. For 25.11, we provided a controller action for repairing the container fields in order to allow the obsolete files to be deleted. This controller action would need to be manually hit to do the repair. This PR adds an upgrade script so data will get repaired for everyone.Related Pull Requests
Changes
FileContentService.fixContainerForExpDataFilesto onlysampletypefiles (since there can be legitimate duplicate references for assay data files)Tasks 📍